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NIH Videocast on Viruses and CFS Featuring Lo and Alter!

Discussion in 'Media, Interviews, Blogs, Talks, Events about XMRV' started by Cort, Jan 28, 2011.

  1. Cort

    Cort Phoenix Rising Founder

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    Now this will be interesting. Dr. Lo/Alter have presumably been working away for the last 3 months or so at either showing XMLV integration into human DNA in their samples or at isolating the virus itself. In about 3 1/2 weeks they'll be giving a 2 hour lecture called "Demystifying CFS - Is there a Virus". That's a long lecture and who knows what come of it. This lecture will be technical - it's directed towards Ph.D students and program managers but it's open to everybody.


    http://videocast.nih.gov/summary.asp?live=9925


     
  2. Jemal

    Jemal Senior Member

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  3. Bob

    Bob

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    Transcription of sections of Alter and Lo presentations

    I posted this on another thread on a different subject, so I thought I ought to copy it onto this thread...

    Demystifying Medicine - Chronic Fatigue Syndrome: Is there a virus?

    http://videocast.nih.gov/Summary.asp?File=16477

    I've watched some of the video, and I've transcribed the most interesting sections that I've watch so far.
    Some of Lo's presentation is a bit disjointed, towards the end of the quote, below, but the only places that i've missed out any text is in places where i've placed 3 dots (...).
    I've bolded the most interesting bits.


    Transcription of Shyh-Ching Lo presentation:

    [83.05]

    "So why did many studies have different findings? This is obviously a very challenging question...

    ...


    "...and the way the clinical sample is prepared, and the processing of this, all can make a difference.

    [83.45]

    And even more possible to me is that there is a variation of the PCR protocol, although everybody says we are following the same PCR assay, but if you look into all the detail, the cycles are different, [indiscernable] temperature slightly different, magnesium concentration slightly different;

    all of this, we really don't know how much that's going to make a difference.

    Today the topic is, is there a virus or not? is the virus responsible, or the causative agent of this, or not?

    That's all very far away at the present time because, when we are looking at this, we obviously are dealing with a very low rate [or 'grade'?] of infection - a very low copy number in the blood,

    and many of these difference can certainly result in the PCR disparities,

    and i just want to mention... the NIH obviously, the NHLBI's, is looking into this, and have this sample, coded sample, sent to different laboratories, and to test it,

    and this is the clinical [or 'critical'?] panel, the CDC's result,

    and obviously ... the four of the patients,

    and depends how the sample is being processed,

    how long the delay of the processing of the sample, and the results are obviously different;

    some are negative and some are positive,

    so this is obviously, they also continue to look into this and try to solve is there any processing of the sample make a difference?

    ..."
    [85.30]

    http://videocast.nih.gov/Summary.asp?File=16477

     
  4. Bob

    Bob

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    Here's more from the video... This is interesting...

    At [96.55]:

    Harvey and Lo sent two of their positive patient samples to the CDC who then couldn't detect the PMRV's in the samples.

    The CDC sent a blind coded negative control sample, from a single patient, to Harvey and Lo, which Harvey and Lo then repeatedly identified as positive, about 15 times. They repeatedly identified the same sample as being positive, even though it was blind coded. So Harvey and Lo detected PMRV in a 'negative control' from the CDC. Lo seems to be saying that this means it isn't a negative sample, but that the CDC just couldn't detect the virus in the sample.

    [My thoughts: if we are talking about contamination here, then it couldn't be in the sample itself, but must enter during the testing stage. But Harvey and Lo's consistent and repeated testing of the negative control sample, as positive, suggests that it isn't contamination.]

    [99.10]

    Lo: "We are pushing to the very end of the sensitivity..."
     
  5. Bob

    Bob

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    I thought this was interesting because it has never occurred to me before (or maybe it did but i forgot that thought!)...

    At [99.30]:

    Lo says that, because they are detecting at the very limits of sensitivity, then one explanation as to why they are detecting XMRV/PMRVs in CFS patients, might be that the viruses could be ubiquitous, but that CFS patients have higher titers than the normal population, just as we do with Herpes and EBV etc., and this means that they can only detect it in CFS patient blood samples and not normal blood samples.

    He wasn't saying this as his opinion, he was just offering it up for discussion, saying it is a possibility, amongst other possibilities.
     
  6. Bob

    Bob

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    Harvey Alter:

    [103.04]

    "If the virus is indeed in the patient, i suggest about a present antibody, and i think it very important that the Whittemore Peterson group has consistently found antibody in the patients, and has found virus that they can culture in these patients; so in their data, they've done the whole gamut; we've had more trouble finding the antibody in our patients; we're working with the NCI group; but despite the fact that the Whittemore Peterson group has been able to culture it and find antibody, people still don't believe that patients were infected; so it's just a difficult field.

    [103.50]

    But that's the issue that we have to address, and if the patient is infected, the next issue is, is it a primary infection that causes the disease, or is it a secondary infection, due to, whatever, amino deficiency, [indiscernible] infection, or something else.

    So how are you going to resolve this?

    Well, the heart and lung institute and the NIAED are conducting separate studies now to assess whether these findings are reproducible and are they specific; and sensitivity is in there as well. But mostly it is to see, are they reproducible and are they specific for this disease.

    So when we suggested exchanging samples between the labs that have divergent findings; we tried to do that, it wasn't sufficient, it wasn't sufficient samples, the answers were not as clear as one would hope.

    But I think the most important thing is what is being done now, particularly in a study that the NIAED is sponsoring.

    Dr Ian Lipkin at Columbia is heading up this study, and the idea is to take classic cases of Chronic Fatigue Syndrome; people that meet the Canadian Criteria, that had an acute onset of disease and then went into the debilitating long term effects; cases that everybody would agree are Chronic Fatigue, to the best that you can agree on that.

    To take those patients, and they are from different places around the country; so they are geographically diverse; Take large volumes of their samples; send them to Dr Lipkin's lab, where they will be separated, and come overnight, and separated into various components, mostly plasma and whole blood, but maybe some PBMC's, and then coded, and the same sample will be coded in triplicate.

    And then panels will be developed, and sent to the labs - who have claimed to find the virus, and those that have claimed not to have found the virus; and those labs will use their own assays, and then see how they break the code.
    And the results will be published, so whatever comes out, positive or negative, the results will be published,
    and the codes will be broken at the coordinating centre.

    [106.34]

    So what are the possible outcomes of that?

    Well, if this cannot be found in these pedigree patients, in the labs who previously reported finding it, then i think that the original findings will have to be considered unconfirmed and contamination will be suspected, but all these samples will be tested for mouse DNA by the best techniques; both the techniques that Dr Lo talked about.

    But if Dr Lo - he is under a lot of pressure - if he doesn't do well on the panels, then we have to say something was awry originally. However, if he does do well, if the panels show that he can consistently detect coded samples from CFS patients, and not from controls, or different ratios on patient controls, then the published findings will have been confirmed.

    And that confirmation will not establish causality, it will just confirm the association, and rule out the contamination issue.

    [107.35]

    And the causality is going to be difficult, it's always difficult, if you don't have an animal model, it's always difficult to prove causality; it may have to be proved by controlled clinical trials using antiretroviral agents.

    And Dr Mikovits has already shown that known antiretroviral agents, the whole XMRV agent is sensitive to two, but not all of the HIV antiretroviral agents.

    [108.02]

    So that's where it's going; this should resolve; this data should be available in the next six months and i think it's the best way to go about it. Up until that time, you can believe what you believe."
     
  7. Bob

    Bob

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    Q&A Session.

    [110.52]

    [Question about viral DNA integration into human genome.]

    [111.15]

    Alter:
    "It's a wonderful question;
    It's very difficult; it's kind of like looking for a needle in a haystack. It can be done.
    People who looked for Beta retroviruses; it took them four years to find an integration site.
    You have no idea where in the genome it might be and you're looking for a low titre; [a] small amount of total genome.
    I'm not a molecular biologist, but i've been told it's very difficult.
    We are working with a group in Canada who are trying to do it, but they don't anticipate a quick answer.
    But that would be a very important thing."

    [112.25]

    Lo:
    "For the prostate, from the tumor, they've been published, and they are flanked by the human sequence.
    But even that, people do challenge that: 'is that truly from a clinical sample, or not, or a contaminant from somewhere?'
    Again that is based on the PCR product, and you do the sequence."


    ---------------------------


    Lo suggests that the discrepancies in testing might be due to the low titres.


    ---------------------------

    Alter talking about CFS, referring to it as a biomedical illness:

    [116.21]

    ...
    "There are similarities in an addisonian patient [referring to Addison's disease],
    there's similarities in a chronic infectious mononucleosis patient.

    It [CFS] smacks of, if not a viral etiology, some kind of neuroendocrine abnormality.
    Something's in there that's doing something.
    That's your final thing:
    There's something doing something!"

    ----------------------------
     
  8. Bob

    Bob

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    I love Alter's quote...
    He means CFS is a real disease, caused by something, and not made up in our heads...
    I think we could use this quote in our community!!!

    "Something's in there that's doing something."
     
  9. free at last

    free at last Senior Member

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    Thanks for all the info here guys, bit of a bombshell, i think. This really proves once and for all that either Alter seems to be able to get consistent positives tested more times than one would reasonably be expected to do, or how the hell can it be found positive that many times. when infact its negative. It seems to me, out of the 15 tests performed. if there was a problem with Alters testing it should have come back negative at some point ? yet the CDC say it was negative. It doesnt mention how many times the CDC tested this apparently Negative sample.

    What could produce a false positive for Alter that many times ? surely contamination was ruled out ? and indeed if there was contamination, it doesnt appear that the CDC seem to be able to detect even contamination as a positive. How do we know this ? Well because if we argue the CDC are right and Alters 15 positive counts were from contamination. Then likely the two positives that were sent by Alter to the CDC should have also been detected as positive. because of such said contamination ? but they didnt. This almost seems to suggest. or i think more likely because of that observation. that the CDCs testing was as Alter suggested likely not detecting the virus at all.

    I wonder if the detections being used were similair to the co operative diagnostics testing. because if they are. then clearly the recent study that has been portrayed as somewhat superior. Looks less superior by the second. There is a problem folks, and i belive the problem seems likely to be with the CDC. otherwise the supposed contamination of the two Positive Alter samples. should have been detected as positive by the CDC. But they were not. So not only does that suggest, that those two samples were not contaminated. but that the CDC were indeed failing to detect positive samples this time around. very very strange
    And what of the WPIs apparently false positive during BWG phase 2. after these very seriouse shortcomings about know negatives. Could they have actually been right all along ?

    There may be reasons why im assuming to much. But one way or the other something is wrong. It still looks more likely to me to be the CDC. Or am i missing something here ?
     
  10. free at last

    free at last Senior Member

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    Hi Bob are you thinking what im thinking, what was it that was said recently in canada, that untill published couldnt be mentioned. But that it was all ticking along nicely. Facebook global XMRV
    If this turned out to be the root of the THE POLITICS WILL SOON BE AT A END statement by Judy ill be gobsmacked. But apparently the reporter said something like jaw dropping. Surely this couldnt all be true. Could it ?
     
  11. Bob

    Bob

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    Yes, I think it's far too early to dismiss XMRV/PMRV. Alter and Lo are still confident about their research.
    What I understood from Alter and Lo is that they are confident about their work, but Alter did not rule out other possibilities, such as contamination, being an explanation for their results. Basically, he's following the evidence; His own evidence. They couldn't explain the discrepancies between all the different results, but Lo did suggest that the most likely reason might be due to low titre levels, extremes of sensitivity, and very small differences in testing processes.
    Harvey said that it all rests on Lo being able to get consistent results during Lipkin's study (and that there is a lot of pressure on him!)
     
  12. Bob

    Bob

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    Yes, the consistency of Lo's testing seems to be a very strong piece of evidence for me. This is assuming that he tested the other 'negative' control sample/s consistently negative. (I don't think that he mentioned this, but I assume that he did, or it wouldn't be so significant. I might rewatch that section to see if I missed something.)

    It is possible that, if there is contamination, it enters the research at the processing/testing stage.
    So Alter and Lo could potentially be detecting contamination that is introduced at a late stage in their testing.
    If this was the case then the CDC would not pick this up because their blood samples would not be contaminated.
     
  13. Bob

    Bob

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    Here's the quote about the coded samples from the CDC:

    [97.30]

    Lo:

    "They [the CDC] had a negative one [sample] and then send to us to test it.

    And I see, for the CDC group of patients, most of them are negative in our hands, [indiscernible],

    But the interesting part; and obviously we don't want to get into the too complicated thing;

    And while they kick in [?], the so called negative control from a single patient, and repeated, I forgot, 15 times, 10 times, or something;

    And that particular sample; we repeatedly identified as positive.

    But that's a coded sample; you know, we did not know that that particular one is a, repeat, coded negative control,

    and that one is positive."



    It is difficult to understand all of Lo's speech in this section of the video, but it does suggest that there were other negative control samples that Lo consistently tested as negative, and that he consistently and repeatedly tested the one negative control as positive.
     
  14. Bob

    Bob

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    Details from Slide 17:

    Mikovits tested 50 patients from England, and found 48% positive for XMRV [by PCR?], 63% positive for XMRV antibody, and tested 78% positive in DERSE culture assay. Antibody found in 4% of controls.

    Hanson tested 20 patients from New York State, and found 55% positive for polytropic sequences.

    http://videocast.nih.gov/Summary.asp?File=16477

    --------------------------------------------------------

    (I don't remember hearing about the Hanson study... I'll have to look that one up.)

    ETA. I think it must be the Hanson/Bell study, but I can't find any info on the results:
    http://forums.aboutmecfs.org/showthread.php?5977-The-Hanson-(Bell-)-XMRV-Study
     
  15. free at last

    free at last Senior Member

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    Here's more from the video... This is interesting...

    At [96.55]:

    Harvey and Lo sent two of their positive patient samples to the CDC who then couldn't detect the PMRV's in the samples

    But they would pick them up if the positives ( contaminated by Alter ) were being sent by Alter to the CDC Bob. if we assume the positives from Alter are false positives produced by contamination at the Alter end. I keep saying Alter sent two positives to the CDC which came back as negastive. this suggests quite a lot Bob. Either those two samples were not contaminated, and the positive result was likely a correct detection. Or they was contaminated by Alter with a false positive detection.

    In which case the CDC should have have detected those two samples as positive. You keep thinking about a clean sample coming from the CDC to Alter. your not thinking about a possible contaminated sample being sent by Alter to the CDC. and the implications of this. or in this case. the lack of implications, because the CDC negative result of those two samples sent by Alter. Suggest quite a lot 1 the sample was not contaminated by Alter. 2 the CDC failed to detect a likely true positive.

    I cant really say it any clearer than that. your looking at what im suggesting, in reverse. Clean samples can get contaminated. contaminated samples cant clean themselves, and its that which allows quite a lot of assumptions to be made. two of which ive made here and elswhere. im not talking about the samples sent by the CDC you cant learn much from that. im talking about the two positives sent by Alter to the CDC you can learn a real lot from that. if one side is positive and the other negative. with the positive detection COMING FIRST The CDC should have have tested this as Positive if ALter had contaminated hes sample at any stage, Yes i was one of those 50 Bob, i tested positive 3 out of the 4 methods used
     
  16. Bob

    Bob

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    Hi free at last,

    I've posted a full answer on the other thread for you...
    http://forums.aboutmecfs.org/showth...nt-Satterfield&p=166527&viewfull=1#post166527

    But, putting it simply, if contamination is a factor, then the samples sent from Harvey/Lo to the CDC might not have been contaminated, if the contamination is introduced at the testing stage.

    I believe that the original samples would be kept separate from the testing stage, and so the original patient samples can't become contaminated if the contamination is introduced at the testing stage. (They separate the original samples into a number of separate phials, before doing any work with them, and only work on one phial at a time.)

    Does that make sense? I don't know if i'm explaining it well.
     
  17. free at last

    free at last Senior Member

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    In that case yes i undersatand, the two samples sent by Alter are not the ones that were handled by Alter at any stage. In which case i aplogize for my assumptions. I assumed they would be the samples that were ACTUALY HANDLED by Alter hence if he contaminated them to produce a false positive reading. they would still be contaminated on route to the CDC. you are infact saying those samples sent to the CDC are not the ones ACTUALLY HANDLED and contaminated with a false positve detection. by Alter is that what you are saying ? apoligize again if my understanding is incomplete
     
  18. Bob

    Bob

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    Yay! Yes! That's it exactly.
    And there's no need to apologise, naturally!
    The beauty of this forum is that we all learn from each other all the time... I learn loads of new things here everyday!
     
  19. Bob

    Bob

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    I'm open minded about the XMRV research, but I believe that the evidence is very strong that we are infected with a retrovirus.
    Did you notice how, early on in the XMRV research, all the 'experts' were saying that Judy had only got false positives, or that she was only detecting endogenous mouse viruses, or mouse DNA, and that XMRV was not a human virus.
    But now, all of those 'experts' are now saying that XMRV is a real virus after all, and it's not a mouse virus...
    And now they are saying that Judy can't possibly be detecting it in CFS patients... But there must be a mistake...
    I wonder in what way they will change their minds next?!?

    Judy is the only person who hasn't changed her mind.
     
  20. free at last

    free at last Senior Member

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    Ive been thinking exactly the same recently Bob, the shift from dead mouse DNA producing false readings ( Huber ect) She contaminated all her samples, then argued Judy must have too ????? She also said Hey the university where the testing was done, had in the past worked with Mice. My God and shes doing another study i think Jeez watch out. the playing feilds seem to get shifted, if one theory starts to fall flat. a new one arrives that explains why it just can not be. There is plenty of concern about xmrv. but lately ive just got a bit more optomistic again. Going back to Alter, at this stage Bob surely he should have run contamination testing, especially as hes results are not agreeing with the CDC. I would find it rather odd if that hasnt happened. if we know that contamination was ruled out, or at least very unlikely. then we are back to square one again. the CDC not detecting true positives. Do we know if contamination testing was done on the discrepent samples ?
     

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